AMBER Archive (2005)

Subject: AMBER: coordinated water molecules deleted when addions

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Mon Aug 01 2005 - 04:20:11 CDT

Dear amber users£¬

There are four water molecules coordinated to MG2+ ion in my peptide.pdb file. Then I combine it with ligand and solvate them in TIP3PBOX. Everything is fine here. But when I add Cl- ions to neutralise this complex, I noticed that one of the coordinated water molecules has been deleted and replaced by Cl-. The coordinated water molecules are very important in this system. How can I add ions to it but keep the coordinated water molecules?

¡¡¡¡¡¡¡¡¡¡¡¡
                                 
Best regards,

Ye Mei
ymei_at_itcc.nju.edu.cn
Institute of Theoretical and Computational Chemistry
Key Laboratory of Mesoscopic Chemistry
School of Chemistry and Chemical Engineering
Nanjing University
Nanjing 210093
P.R.China
2005-08-01

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